Rev Language Reference


dnFossilizedBirthDeathRange

The fossilized birth death range process describes diversification and sampling of extinct species trees under a mixed model of asymmetric, symmetric and anagenetic speciation.

Aliases

  • dnFBDRP

Usage

dnFossilizedBirthDeathRange(RealPos rootAge/originAge, RealPos lambda, RealPos mu, RealPos psi, Probability rho, RealPos lambda_a, Probability beta, RealPos[] timeline, Natural k, String condition, Taxon[] taxa, Bool bounded, Bool binary, Bool extended)

Arguments

rootAge/originAge : RealPos (pass by const reference)
The start time of the process.
lambda : RealPos (pass by const reference)
The (asymmetric) speciation rate(s).
mu : RealPos (pass by const reference)
The extinction rate(s).
Default : 0
psi : RealPos (pass by const reference)
The fossil sampling rate(s).
Default : 0
rho : Probability (pass by const reference)
The extant sampling fraction.
Default : 1
lambda_a : RealPos (pass by const reference)
The anagenetic speciation rate(s).
Default : 0
beta : Probability (pass by const reference)
The probability of symmetric speciation.
Default : 0
timeline : RealPos[] (pass by const reference)
The rate interval change times of the piecewise constant process.
Default : NULL
k : Natural (pass by const reference)
The fossil observation counts (total or [interval] or [interval][species]).
Default : NULL
condition : String (pass by value)
The condition of the process.
Default : time
Options : time|survival
taxa : Taxon[] (pass by const reference)
The taxa used for initialization.
bounded : Bool (pass by value)
Treat first and last occurrence ages as known range boundaries?
Default : TRUE
binary : Bool (pass by value)
Treat fossil counts as binary presence/absence data?
Default : FALSE
extended : Bool (pass by value)
Treat tip nodes as extinction events?
Default : FALSE

Domain Type

Details

Fossil species samples are represented by their sampled stratigraphic ranges, consisting of a first and last occurrence, and sample count data. Sampling data may be provided by species, time interval, or both depending on the sampling model assumed. The distribution may describe either sampled trees, in which unsampled tips represent sampling events, or extended trees in which tips represent extinction events.

See Also